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Search: Posts Made By: rwenang
Forum: Bioinformatics 07-10-2011, 10:05 PM
Replies: 30
Views: 9,474
Posted By rwenang
It should do okay. Though, I think what you need...

It should do okay. Though, I think what you need to worry about is the RAM if you are going to assemble big genome.
Forum: Bioinformatics 05-23-2011, 02:08 AM
Replies: 3
Views: 1,338
Posted By rwenang
There are some tools which predict the precursor...

There are some tools which predict the precursor mirna structure from the sequence. If im not mistaken they used HMM to do that, but I cannot remember the name of the tool.
Forum: Bioinformatics 05-22-2011, 07:53 PM
Replies: 9
Views: 3,743
Posted By rwenang
Ah yes, its not 16s metagenomics. Definitely need...

Ah yes, its not 16s metagenomics. Definitely need another cup of coffee :p
Forum: Bioinformatics 05-22-2011, 07:26 PM
Replies: 9
Views: 3,743
Posted By rwenang
you can try QIIME to process the data....

you can try QIIME to process the data. http://qiime.sourceforge.net/index.html
Forum: Bioinformatics 03-30-2011, 02:29 AM
Replies: 1
Views: 1,955
Posted By rwenang
CLIP-seq dataset

Dear All,

I'm currently working on a HITS-CLIP project in our lab, and we wanted to do some comparison with previous projects. However, I just found out that I cannot find/download the datasets...
Forum: De novo discovery 03-07-2011, 01:14 AM
Replies: 12
Views: 6,836
Posted By rwenang
in transcriptome, the reads come from many dna...

in transcriptome, the reads come from many dna transcripts, which is why the assembler uses different k-mer sizes to try to assemble them correctly. Meanwhile, in denovo assembly, the reads come from...
Forum: Bioinformatics 03-07-2011, 12:44 AM
Replies: 7
Views: 2,663
Posted By rwenang
try "bioinformatics for dummies". it might...

try "bioinformatics for dummies". it might help.
Forum: De novo discovery 03-07-2011, 12:42 AM
Replies: 12
Views: 6,836
Posted By rwenang
In transcriptome, specifying different k-mers is...

In transcriptome, specifying different k-mers is applied to accommodate transcripts with different sizes.
Forum: De novo discovery 03-07-2011, 12:16 AM
Replies: 12
Views: 6,836
Posted By rwenang
you mean the de bruijn approach? supposedly it...

you mean the de bruijn approach? supposedly it resolves repeats better than overlapping method (OLC)
Forum: Bioinformatics 02-06-2011, 08:15 PM
Replies: 2
Views: 2,527
Posted By rwenang
it will be a simple identity match (97%).

it will be a simple identity match (97%).
Forum: Bioinformatics 02-01-2011, 12:12 AM
Replies: 2
Views: 2,527
Posted By rwenang
clustering paired-end reads

Hi Guys,

Anybody can tell me which tools to use for paired-end reads clustering?
In addition, I would like to do the clustering for 5 different datasets.

I looked through UCLUST and CD-HIT,...
Forum: Introductions 01-30-2011, 07:15 PM
Replies: 8
Views: 5,971
Posted By rwenang
Try trans-abyss or oases. They are more...

Try trans-abyss or oases. They are more specialized in assembling transcriptome compared to genome assembler (SOAP de novo, velvet, abyss).
Forum: Bioinformatics 01-24-2011, 06:24 PM
Replies: 12
Views: 7,259
Posted By rwenang
I used it with a 36GB machine, but I never tried...

I used it with a 36GB machine, but I never tried it with a 100x data before. There is a 30day trial license if you want to try at http://www.clcbio.com.
and for the record i dont get any incentive...
Forum: Bioinformatics 01-24-2011, 01:55 AM
Replies: 12
Views: 7,259
Posted By rwenang
I agree that its not an encouraging number,...

I agree that its not an encouraging number, though the problem most likely lies in soap denovo configuration rather than the data itself. I used soap denovo several times and found it a bit hard to...
Forum: Bioinformatics 01-18-2011, 07:35 PM
Replies: 3
Views: 2,109
Posted By rwenang
'Targeted capture and massively parallel...

'Targeted capture and massively parallel sequencing of 12 human exomes'. A quick search on wikipedia will direct you to other references.
Forum: Bioinformatics 12-14-2010, 12:08 AM
Replies: 1
Views: 1,501
Posted By rwenang
It depends on what is your definition of false...

It depends on what is your definition of false positive mapping. Due to repeats, some reads can be mapped into several locations with the same level of quality. One way is to employ some sort of...
Forum: Bioinformatics 12-13-2010, 12:36 AM
Replies: 2
Views: 7,282
Posted By rwenang
If I remember correctly, there are pictar4way and...

If I remember correctly, there are pictar4way and pictar5way tracks in the UCSC browser. As i recall, the tracks were quite outdated.
Forum: 454 Pyrosequencing 12-12-2010, 08:43 PM
Replies: 11
Views: 2,517
Posted By rwenang
this...

this (http://www.ncbi.nlm.nih.gov/pubmed/19156205) might be helpful...
Forum: RNA Sequencing 12-07-2010, 12:47 AM
Replies: 4
Views: 2,479
Posted By rwenang
yes they can, but i never use them though so i...

yes they can, but i never use them though so i dont know about the quality. Read about it on their paper "De novo assembly and analysis of RNA-seq data".
Forum: Bioinformatics 12-07-2010, 12:04 AM
Replies: 147
Views: 58,764
Posted By rwenang
Hi Kaiye, interesting tool you got there....

Hi Kaiye,

interesting tool you got there. anyway, have you publish the method? I am curious about one thing, say you have 1 read, you will grow the pattern until you cannot get a match, then you...
Forum: RNA Sequencing 12-06-2010, 11:46 PM
Replies: 4
Views: 2,479
Posted By rwenang
on top of my head, you can use trans-abyss.

on top of my head, you can use trans-abyss.
Forum: Bioinformatics 10-25-2010, 08:33 PM
Replies: 0
Views: 1,294
Posted By rwenang
Ideal Reads for Different NGS Applications

Hi All,

I'm in a position where I need to advice biologists which technology is suitable for their experiment purpose. Is there any study which explores the ideal condition of reads (or rule of...
Forum: Bioinformatics 10-21-2010, 07:16 PM
Replies: 3
Views: 2,154
Posted By rwenang
Since you already tried mapping and got few...

Since you already tried mapping and got few alignments, I don't think assembly will produce a better result. However, as francois.sabot said, you can try relaxing the mapping criteria (higher...
Forum: Metagenomics 10-21-2010, 01:24 AM
Replies: 12
Views: 6,055
Posted By rwenang
Is it a 16S or WGS sample?

Is it a 16S or WGS sample?
Forum: Bioinformatics 10-07-2010, 07:20 PM
Replies: 1
Views: 2,763
Posted By rwenang
Hi, just my 2cents: "I expect that if...

Hi, just my 2cents:

"I expect that if Bowtie's options are set to only align unique reads with no mismatches, there shouldn't be a difference between whole-genome and single chromosome index...
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